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Summarized voucher information on vertebrate genomes

Citation

Chakrabarty, Prosanta; Buckner, Janet; Faircloth, Brant (2021), Summarized voucher information on vertebrate genomes, Dryad, Dataset, https://doi.org/10.5061/dryad.6wwpzgmz4

Abstract

A voucher is a permanently preserved specimen that is maintained in an accessible collection. In genomics, vouchers serve as the physical evidence for the taxonomic identification of genome assemblies. Unfortunately, the vast majority of vertebrate genomes stored in NCBI do not refer to voucher specimens. Here, we urge researchers generating new genome assemblies to deposit voucher specimens in accessible, permanent research collections, and to link these vouchers to publications, public databases, and repositories. We also encourage scientists to deposit voucher specimens in order to recognize the work of local field biologists and promote a diverse and inclusive knowledge base, and we recommend best practices to in voucher deposition to prevent taxonomic errors and ensure reproducibility and legality in genetic studies.

Methods

We surveyed the NCBI list of vertebrate genomes with an assembly publication date up to January 1, 2020 (https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/vertebrates) and coverage of 30X or greater. (Although we focused on reviewing vertebrate genomes, the lack of vouchers is a problem among genetic sequences submitted from many different types of organisms). When available, we also cross-checked the original publications reporting the genome sequences for references to a deposited voucher specimen. There were times we found no papers associated with the genome and no contact information could be found on NCBI. Summarized information on the genomes included in this assessment can be found in the supplemental information.

Funding

National Science Foundation, Award: IOB-1754417